Contacts of the helix formed by residues 959 - 970 (chain D) in PDB entry 3IKM
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 959 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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958D GLY* 1.3 66.5 - - - -
960D PRO* 1.4 71.2 - - + +
962D ALA* 3.1 2.4 - - - +
963D GLU* 2.7 34.2 + - - +
982D ALA* 2.7 35.0 + - - +
983D GLN* 2.9 34.7 + - - +
986D TYR* 3.6 33.6 - - + +
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Residues in contact with PRO 960 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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957D ALA* 6.1 0.2 - - + -
958D GLY 2.6 5.8 - - - +
959D GLN* 1.4 95.6 - - + +
961D PHE* 1.3 83.4 + - + +
962D ALA 2.9 2.4 + - - -
963D GLU* 2.9 17.0 + - + +
964D ARG* 2.8 30.5 + - + +
1049D TRP* 4.3 18.6 - - + -
1050D LYS* 6.3 1.1 - - + -
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Residues in contact with PHE 961 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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956D GLY* 5.6 0.9 - - - -
957D ALA* 3.1 46.2 - - + +
958D GLY 3.2 6.4 + - - -
960D PRO* 1.3 77.8 - - + +
962D ALA* 1.3 61.3 + - - +
964D ARG* 3.9 2.8 - - - +
965D LEU* 3.1 35.4 + - + +
1049D TRP* 2.9 69.8 - + + -
1052D GLY* 5.1 2.0 - - - -
1053D THR* 4.1 26.6 + - - +
1056D GLU* 5.1 7.9 - - + -
1094D THR* 4.1 17.3 - - + -
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Residues in contact with ALA 962 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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949D PHE* 6.6 0.2 - - - -
953D ARG* 6.5 0.9 - - + -
957D ALA 4.4 0.2 + - - -
958D GLY* 3.7 8.7 + - - -
959D GLN 3.1 20.4 - - - +
961D PHE* 1.3 79.3 - - - +
963D GLU* 1.3 66.6 + - - +
965D LEU* 3.3 7.8 + - - +
966D LEU* 3.0 25.1 + - - +
982D ALA* 3.2 19.1 - - + +
985D MET* 4.8 9.9 - - + -
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Residues in contact with GLU 963 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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959D GLN* 2.7 35.3 + - - +
960D PRO* 3.1 22.9 - - + +
962D ALA* 1.3 72.2 - - - +
964D ARG* 1.3 52.7 + - + +
966D LEU* 3.3 4.6 - - - +
967D MET* 2.7 37.4 + - - +
975D GLN* 4.8 9.9 + - - +
978D ALA* 3.1 28.7 - - + +
979D ALA* 3.5 32.5 + - - +
982D ALA* 3.0 5.8 - - + +
983D GLN* 4.4 6.4 - - - +
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Residues in contact with ARG 964 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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732D TYR* 4.6 14.3 - - - -
755D LYS* 3.7 36.1 - - + +
960D PRO* 2.8 24.0 + - + +
961D PHE* 3.9 4.9 - - - +
963D GLU* 1.3 73.9 - - + +
965D LEU* 1.3 57.4 + - - +
967D MET* 3.1 6.6 + - - +
968D GLN* 2.6 43.0 + - - +
1050D LYS* 4.2 40.1 + - - +
1053D THR* 4.2 25.7 - - + +
1054D GLU* 5.1 6.7 + - - +
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Residues in contact with LEU 965 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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945D HIS* 5.4 1.6 - - + -
949D PHE* 5.0 19.7 - - + -
952D GLY* 6.2 2.9 - - - -
961D PHE* 3.1 22.2 + - + +
962D ALA* 3.7 6.5 - - - +
964D ARG* 1.3 79.5 - - + +
966D LEU* 1.3 67.8 + - - +
968D GLN* 3.3 10.3 + - + +
969D PHE* 3.1 38.6 + - + -
1053D THR* 5.5 6.5 - - + -
1056D GLU* 6.4 2.5 - - + -
1057D MET* 4.4 27.4 - - + -
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Residues in contact with LEU 966 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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941D ILE* 6.1 1.3 - - + -
945D HIS* 5.4 4.9 - - - +
949D PHE* 6.4 2.7 - - + -
962D ALA 3.0 15.8 + - - +
963D GLU* 3.3 7.4 - - - +
965D LEU* 1.3 79.6 - - - +
967D MET* 1.3 57.2 + - + +
969D PHE* 2.8 1.2 + - - -
970D ASN* 2.4 71.5 + - + +
978D ALA* 4.3 11.7 - - + +
981D LYS* 3.8 30.7 - - + -
982D ALA* 4.0 7.9 - - - +
985D MET* 3.9 29.6 - - + -
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Residues in contact with MET 967 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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734D HIS* 5.4 12.8 - - + -
963D GLU 2.7 14.2 + - - +
964D ARG* 3.2 13.2 - - - +
966D LEU* 1.3 72.1 - - + +
968D GLN* 1.3 70.5 + - + +
970D ASN* 2.8 23.9 - - + +
971D HIS 4.5 6.6 - - - +
973D LEU* 4.4 2.7 - - + -
974D THR* 3.0 34.1 - - - +
975D GLN* 2.8 32.8 - - + -
978D ALA* 3.1 21.5 - - + -
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Residues in contact with GLN 968 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753D PRO* 4.0 11.4 - - - +
755D LYS* 3.8 33.5 - - - +
756D ASP* 3.5 24.7 + - - +
770D PHE* 2.5 44.7 - - + -
774D MET* 5.2 0.5 - - - +
964D ARG* 2.6 40.7 + - - +
965D LEU* 3.5 14.4 - - + +
967D MET* 1.3 77.2 - - + +
969D PHE* 1.3 66.8 + - + +
970D ASN 3.4 3.5 - - - +
971D HIS* 5.1 0.9 + - - -
1053D THR* 4.8 8.9 - - - +
1057D MET* 5.6 3.6 - - - -
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Residues in contact with PHE 969 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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756D ASP* 6.1 0.7 - - - -
770D PHE* 4.4 7.9 - + - -
773D LYS* 4.0 41.7 - - + -
774D MET* 6.5 0.2 - - - -
945D HIS* 2.9 43.1 - + + -
965D LEU* 3.1 27.3 + - + -
966D LEU 2.8 8.9 + - - +
968D GLN* 1.3 78.2 - - + +
970D ASN* 1.3 60.3 + - - +
971D HIS* 3.0 21.3 - - - -
1065D ALA* 6.5 0.4 - - + -
1067D SER* 6.0 2.7 - - - -
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Residues in contact with ASN 970 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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941D ILE* 3.9 23.4 - - - +
945D HIS* 4.9 5.9 + - - -
966D LEU* 2.4 76.2 + - + +
967D MET* 2.8 24.8 - - + +
968D GLN 3.4 3.8 - - - +
969D PHE* 1.3 74.3 - - - +
971D HIS* 1.3 73.9 + - - +
973D LEU* 5.2 15.3 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il